Parameter Table

keyword	variable name	allowed values	default
mode	mode	single search database	single
receptor_sphere_file	clufil	filename	none
cluster_numbers	nclus	c1 c2 c3...	none
ligand_type	ligtyp	c, coordinates s, spheres	c
ligand_atom_file	ligfil	filename	none
# (if ligand_type = s) ligand_sphere_file	lgsfil	filename	none

Parameter Descriptions

mode

indicates the type of run to be performed. It has three acceptable values, single, search, or database, where the latter two are equivalent. Uppercase letters are also acceptable, but not a mixture of upper and lower cases. SINGLE ligand mode will produce multiple orientations of a single ligand molecule, and SEARCH mode will produce the single best orientation of each of the top-scoring molecules from the input database.

receptor_sphere_file

is followed by the file containing the receptor sphere center coordinates organized into clusters of overlapping spheres. This file is created by sphgen or cluster.

cluster_numbers

should be followed by one or more integers, giving the numbers of the receptor sphere clusters of interest. More than one cluster can be listed here, allowing for docking to a series of clusters in a single run. The clusters are used sequentially and independently. The number of clusters is determined automatically and equals the number of integers found in the 80-character line.

ligand_type

indicates whether ligand atomic coordinates or ligand sphere centers will be used for matching. If ligand_type does not equal s or S, coordinates will be used.

ligand_atom_file

gives the name of the input file containing ligand coordinates. In SINGLE mode, the file should contain one molecule, whereas in SEARCH it should contain the database to be examined. In SINGLE mode, any of the following formats is currently acceptable: standard PDB format, extended PDB format, SYBYL ASCII (MOL2) format, and any of the DOCK database formats. In SEARCH mode, only DOCK database format can be used. DOCK database format has existed in different versions: with or without charges, with atomic numbers, with van der Waals types instead of atomic numbers, with or without atom labeling (coloring) information. The DOCK database version is automatically determined, and is accepted whenever it is compatible with the scoring option (i.e. charges must be present if electrostatic or force-field scoring is selected, and van der Waals types rather than atomic numbers must be present if force-field scoring is selected). The extended PDB format, SYBYL ASCII format, and DOCK database format from mol2db are all compatible with any scoring option. Even when ligand sphere centers are used for matching (SINGLE mode), the atomic coordinates are necessary because the rotation/translation is applied to them (not the sphere center coordinates) in generating output. If the data supplied is inconsistent with the scoring option selected, an error message is written to OUTDOCK. Database files are created using mkdb, which converts Cambridge Structural Database format (for contact scoring only), or mol2db, which converts SYBYL ASCII format.

ligand_sphere_file

gives the name of the file containing ligand sphere center coordinates, created by sphgen or cluster.